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scverse

Foundational tools for omics data in the life sciences
README.md

Welcome to scverse®!

scverse

scverse® is a community that develops and maintains foundational tools for single-cell omics data analysis in primarily Python.

Here's how to get started:

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  1. scanpy scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    Python 2.6k 798

  2. anndata anndata Public

    Annotated data.

    Python 780 220

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 482

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 608 126

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 403 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 352 68

Repositories

Showing 10 of 97 repositories
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 7 0 Updated Oct 19, 2026
  • anndata-rs Public
    scverse/anndata-rs's past year of commit activity
    Rust 50 BSD-3-Clause 17 11 5 Updated Oct 19, 2026
  • scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    scverse/scanpy's past year of commit activity
    Python 2,590 BSD-3-Clause 798 447 (3 issues need help) 109 Updated Oct 19, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 780 BSD-3-Clause 220 187 (4 issues need help) 90 Updated Oct 19, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 28 11 2 Updated Oct 19, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 12 BSD-3-Clause 0 37 2 Updated Oct 19, 2026
  • acumen Public

    A toolkit to test, validate, and improve agentic skills.

    scverse/acumen's past year of commit activity
    Python 18 MIT 1 2 1 Updated Oct 19, 2026
  • spatialdata-io Public
    scverse/spatialdata-io's past year of commit activity
    Python 107 BSD-3-Clause 65 70 14 Updated Oct 19, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 5 1 Updated Oct 18, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 403 MIT 54 13 14 Updated Oct 18, 2026
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